Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004166.1 Kokia drynarioides strain JFW-HI SEQ_117395, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 9198
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Found at i:4676 original size:14 final size:13
Alignment explanation
Indices: 4657--4706 Score: 66
Period size: 13 Copynumber: 3.8 Consensus size: 13
4647 AAAATGTGGG
4657 TTTTCTTTTTTCTT
1 TTTTCTTTTTT-TT
4671 TTTTCTTTTTTTT
1 TTTTCTTTTTTTT
*
4684 TTTT-TACTTTTTT
1 TTTTCT-TTTTTTT
4697 TTTTCTTTTT
1 TTTTCTTTTT
4707 ACTCTACCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
12 1 0.03
13 19 0.59
14 12 0.38
ACGTcount: A:0.02, C:0.10, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTCTTTTTTTT
Found at i:4682 original size:15 final size:14
Alignment explanation
Indices: 4657--4700 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
4647 AAAATGTGGG
*
4657 TTTTCTTTTTTCTT
1 TTTTCTTTTTTTTT
4671 TTTTCTTTTTTTTT
1 TTTTCTTTTTTTTT
4685 TTTTACTTTTTTTTT
1 TTTT-CTTTTTTTTT
4700 T
1 T
4701 CTTTTTACTC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
14 17 0.61
15 11 0.39
ACGTcount: A:0.02, C:0.09, G:0.00, T:0.89
Consensus pattern (14 bp):
TTTTCTTTTTTTTT
Found at i:4706 original size:7 final size:7
Alignment explanation
Indices: 4657--4700 Score: 63
Period size: 7 Copynumber: 6.3 Consensus size: 7
4647 AAAATGTGGG
4657 TTTTCTT
1 TTTTCTT
4664 TTTTCTT
1 TTTTCTT
4671 TTTTCTT
1 TTTTCTT
*
4678 TTTTTTT
1 TTTTCTT
4685 TTTTACTT
1 TTTT-CTT
4693 TTTT-TT
1 TTTTCTT
4699 TT
1 TT
4701 CTTTTTACTC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
6 4 0.12
7 24 0.71
8 6 0.18
ACGTcount: A:0.02, C:0.09, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTCTT
Found at i:5620 original size:18 final size:18
Alignment explanation
Indices: 5597--5643 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
5587 TTAAGTACAA
*
5597 AAATATACAAT-TTTTATT
1 AAATATA-AATATTATATT
5615 AAATATAAATATTATATT
1 AAATATAAATATTATATT
*
5633 AAATAAAAATA
1 AAATATAAATA
5644 ACAAAAATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 3 0.12
18 23 0.88
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATATAAATATTATATT
Found at i:7490 original size:31 final size:32
Alignment explanation
Indices: 7454--7595 Score: 109
Period size: 33 Copynumber: 4.6 Consensus size: 32
7444 GTACCCCAAA
* * *
7454 AAGTTTAAGTACCAACTT-CAAAAAAGGTGTC
1 AAGTTTAAGTACCAAATTAAAAAAAAAGTGTC
* *
7485 AAGTTTAGGTAGCAAATTAGAAAAAAAAGTGTC
1 AAGTTTAAGTACCAAATTA-AAAAAAAAGTGTC
* * * **
7518 AAGTTTGAGTACCAAGTTGAACCAAAA-----
1 AAGTTTAAGTACCAAATTAAAAAAAAAGTGTC
*
7545 AAGTTTAAGTACTAAATTAAAAAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAAAAAAAAAGTGTC
*
7577 AAG-TTCAGATACCAAATTA
1 AAGTTTAAG-TACCAAATTA
7596 TATTAAAGCT
Statistics
Matches: 83, Mismatches: 20, Indels: 15
0.70 0.17 0.13
Matches are distributed among these distances:
27 21 0.25
31 19 0.23
32 18 0.22
33 25 0.30
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.25
Consensus pattern (32 bp):
AAGTTTAAGTACCAAATTAAAAAAAAAGTGTC
Found at i:7545 original size:34 final size:34
Alignment explanation
Indices: 7472--7595 Score: 90
Period size: 32 Copynumber: 3.9 Consensus size: 34
7462 GTACCAACTT
*
7472 CAAAAAAGGTGTCAAGTTTAGGTAGCAAATTAGAA
1 CAAAAAA-GTGTCAAGTTTAGGTACCAAATTAGAA
*
7507 -AAAAAAGTGTCAAGTTT-GAGTACCAAGTT-GAA
1 CAAAAAAGTGTCAAGTTTAG-GTACCAAATTAGAA
* * *
7539 C-CAAAA-----AAGTTTAAGTACTAAATTA-AA
1 CAAAAAAGTGTCAAGTTTAGGTACCAAATTAGAA
* *
7566 -AAAAAAGTGTCAAGTTCAGATACCAAATTA
1 CAAAAAAGTGTCAAGTTTAGGTACCAAATTA
7596 TATTAAAGCT
Statistics
Matches: 68, Mismatches: 11, Indels: 23
0.67 0.11 0.23
Matches are distributed among these distances:
27 20 0.29
32 23 0.34
33 19 0.28
34 6 0.09
ACGTcount: A:0.48, C:0.10, G:0.17, T:0.24
Consensus pattern (34 bp):
CAAAAAAGTGTCAAGTTTAGGTACCAAATTAGAA
Done.